Contacts of the helix formed by residues 118 - 129 (chain B) in PDB entry 5U8T
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B VAL* 3.4 23.6 - - + +
23B GLU* 3.4 26.9 - - - +
116B PRO* 2.7 16.5 + - - +
117B TRP* 1.3 102.5 - - + +
119B TRP* 1.3 63.3 + - - +
120B LEU 3.6 1.8 - - - -
121B VAL* 3.3 16.0 + - - +
122B LEU* 3.1 38.9 + - + +
174B SER* 4.5 1.1 - - - -
175B LEU* 6.2 0.4 - - - -
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Residues in contact with TRP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B TRP* 3.9 30.4 - + + -
98B LEU* 6.5 0.4 - - + -
115B LEU* 3.7 27.1 - - + +
116B PRO* 4.4 10.8 - - + -
117B TRP* 3.7 14.6 - - - -
118B ASN* 1.3 76.6 + - - +
120B LEU* 1.3 89.4 + - + +
122B LEU* 2.8 14.3 + - - +
123B ALA* 2.7 37.1 + - + +
145B ILE* 4.5 24.5 - - + -
148B LEU* 3.7 32.3 - - + -
149B ARG* 4.6 9.6 - - - -
152B ARG* 4.3 1.1 - - - -
174B SER* 3.1 31.7 - - - -
177B GLU* 2.9 24.5 - - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ASN 3.4 0.8 + - - -
119B TRP* 1.3 116.6 - - + +
121B VAL* 1.3 63.9 + - - +
123B ALA* 3.2 8.7 + - - +
124B ARG* 3.1 22.9 + - - +
145B ILE* 5.4 7.9 - - + +
149B ARG* 4.2 26.5 - - + +
174B SER* 3.9 2.9 - - - -
176B LEU* 3.6 38.8 - - + -
177B GLU* 3.5 30.1 - - + -
190C TRP* 4.5 1.8 - - - -
191C MET* 5.2 6.6 - - + +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.5 11.0 - - + -
17B GLN* 3.7 19.1 - - + -
20B VAL* 3.6 31.2 - - + -
118B ASN* 3.4 14.6 - - - +
119B TRP 3.2 0.4 - - - -
120B LEU* 1.3 78.4 - - - +
122B LEU* 1.3 57.0 + - - +
124B ARG* 3.3 1.7 + - - +
125B ILE* 2.8 47.2 + - + +
176B LEU* 3.5 28.5 - - + +
190C TRP* 3.9 16.8 - - + -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 4.5 11.0 - - + -
23B GLU* 6.5 0.7 - - + -
25B ILE* 5.1 15.3 - - + -
73B LEU* 4.8 15.5 - - + -
90B PRO* 5.4 5.2 - - + -
92B TRP* 4.3 25.4 - - + +
93B LEU* 5.8 0.2 - - - -
116B PRO* 5.0 0.9 - - + -
118B ASN* 3.1 46.8 + - + +
119B TRP* 2.8 17.9 + - - +
121B VAL* 1.3 70.8 - - - +
123B ALA* 1.3 55.8 + - - +
125B ILE* 3.4 5.1 - - - +
126B LEU* 2.8 56.2 + - + +
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B TRP* 5.7 2.0 - - + -
93B LEU* 5.2 9.1 - - + +
119B TRP* 2.7 16.6 + - + +
120B LEU* 3.2 13.9 - - - +
122B LEU* 1.3 72.1 - - - +
124B ARG* 1.3 64.1 + - - +
126B LEU* 3.9 0.8 - - - -
127B PHE* 2.9 53.9 + - + -
145B ILE* 5.1 17.5 - - + -
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN* 4.0 5.3 + - - +
120B LEU 3.1 6.8 + - - +
121B VAL 3.9 0.2 - - - +
123B ALA* 1.3 78.3 - - - +
125B ILE* 1.3 63.6 + - - +
127B PHE* 3.8 6.5 - - - +
128B ASN* 2.8 58.3 + - - +
190C TRP* 2.6 86.0 + - + +
191C MET* 3.1 24.6 + - - +
192C PHE 4.2 0.2 - - - +
193C LYS* 4.3 21.6 + - - +
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN* 5.8 1.3 - - + +
20B VAL* 4.7 4.7 - - + -
21B GLU* 4.2 19.1 - - + +
73B LEU* 3.7 37.0 - - + -
77B LEU* 4.5 15.5 - - + -
121B VAL* 2.8 47.2 + - + +
122B LEU* 3.4 8.1 - - + +
124B ARG* 1.3 84.9 - - - +
126B LEU* 1.3 78.9 + - + +
128B ASN* 3.5 18.2 - - - +
129B LYS* 3.7 11.8 + - - +
130B ALA 4.5 0.9 + - - -
190C TRP* 5.3 0.7 - - + -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 5.9 0.7 - - + -
73B LEU* 4.8 10.1 - - + -
87B ILE* 4.4 16.4 - - + -
90B PRO* 4.0 24.5 - - + -
93B LEU* 4.5 7.9 - - + -
122B LEU* 2.8 38.7 + - + +
123B ALA 4.0 1.6 - - - +
125B ILE* 1.3 85.2 - - + +
127B PHE* 1.3 64.4 + - + +
130B ALA* 2.5 44.6 + - + -
131B LYS 2.9 7.7 + - - -
134B PHE* 3.4 36.6 - - + -
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 5.1 4.5 - - + -
123B ALA* 2.9 42.3 + - + +
124B ARG* 3.9 5.4 - - - +
126B LEU* 1.3 76.0 - - - +
128B ASN* 1.3 63.6 + - - +
131B LYS* 3.3 28.5 - - + +
134B PHE* 3.5 35.7 - + - -
137B PRO* 4.1 13.0 - - + -
141B LEU* 4.3 23.1 - - + -
142B ARG* 3.4 45.5 - - + +
145B ILE* 5.2 5.6 - - + -
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Residues in contact with ASN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ARG* 2.8 65.1 + - - +
125B ILE* 3.5 6.7 - - - +
126B LEU 3.2 0.2 - - - -
127B PHE* 1.3 78.4 - - - +
129B LYS* 1.3 84.6 + - - +
131B LYS* 4.6 7.8 - - - +
193C LYS* 5.8 2.6 + - - +
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LEU* 3.6 43.3 - - + +
80B LYS* 3.3 17.9 + - + +
81B GLN* 5.1 19.5 - - + +
125B ILE* 3.7 8.8 + - - +
126B LEU 3.1 1.0 + - - -
128B ASN* 1.3 110.3 + - - +
130B ALA* 1.3 51.8 + - - +
131B LYS* 2.8 25.3 + - - +
132B ASP* 2.8 16.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il